Tag Archives: bioinformatics

Forging research partnerships between the BecA-ILRI Hub and Earlham Institute

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By Joyce Nzioki, Research associate-bioinformatics at the Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub

Joyce Nzioki (left) and Fracnesca Stomeo at the Earlham Institute in Norwich, UK

Joyce Nzioki (left) and Fracnesca Stomeo at the Earlham Institute in Norwich, UK

From 1-13 July 2017, capacity building scientist Francesca Stomeo and I visited the Earlham Institute in Norwich, UK. Our mission was to explore ways of strengthening the budding partnership between the BecA-ILRI Hub and Earlham Institute as well as to gain knowledge that will improve the Hub’s genomics and bioinformatics platform.

We had an intense one and a half week of meetings and interaction with the institute’s genomics and bioinformatics specialists, with guidance of our hosts Anthony Hall, head of plant genomics and post-doctoral scientist Jose de Vega. There was much to learn about different aspects of genomics and bioinformatics, particularly in terms of lab and bioinformatics protocols and systems.

It was very exciting to share experiences on our research and training opportunities, and make potential connections for joint activities in the near future. The discussion we had with the project leader-bioinformatic algorithms, Bernardo Clavijo was invaluable in planning for the BecA-ILRI Hub annual advanced bioinformatics workshop that will take place in October this year. I am really glad that Clavijo will be among the trainers for that workshop.

Discussions on work by national agricultural research system (NARS) research fellows conducted at the BecA-ILRI Hub highlighted potential areas of collaborative research to enhance food safety and security in Africa including: improved conservation of fish, understanding drug resistance in Salmonella, plant transformation and exploiting various under-utilized African crop species. We were also challenged to consider introducing the portable Oxford Nano Pore sequencing technology to serve our partners who may not be able to purchase the bigger high through put sequencing machines.

From the visit to Earlham Institute, I saw a clear need for improved bioinformatics capacity to fulfil the potential of modern biosciences in Africa. Bioinformatics training—a key component of the BecA-ILRI Hub’s remit—is central to the training conducted at the Norwich Research Park (NRP), of which the Earlham Institute is a partner. We had fruitful discussions on strategies to empower a cohort of bioinformaticians in Africa with hands-on training in 2018.

I look forward to many joint research and training activities with scientists in Earlham Institute starting with the bioinformatics workshop in October!

The bioinformatics lab at the Earlham Institute in Norwich, UK

The sequencing facility at the Earlham Institute in Norwich, UK

About the author:
Joyce Nzioki is a bioinformatics analyst providing bioinformatics support to various on-going genomics projects at the BecA-ILRI Hub. She holds a Masters in Bioinformatics from Rhodes University in South Africa and a Bachelor’s degree in Biomedical Technology from the University of Nairobi, Kenya. Through her MSc studies, she gained skills in working in a Linux environment, Python programming, mathematical and statistical applications to biology and bioinformatics (R and Matlab), structural bioinformatics, genomics and proteomics.

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Making agricultural sense of data in Sudan: The BecA-ILRI Hub bioinformatics workshop in Khartoum

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From 1 December to 6 December 2014, the BecA-ILRI Hub held a bioinformatics workshop in Khartoum, Sudan. Mark Wamalwa, a post-doctoral scientist in bioinformatics and Joyce Nzioki, a bioinformatics analyst from the BecA-ILRI Hub, in collaboration with Andreas Gisel from the International Institute of Tropical Agriculture (IITA), Nigeria and Etienne De Villiers from the Kenyan Medical Research Institute (KEMRI) Wellcome Trust, Kilifi-Kenya.

BecA bioinformatics workshop in Sudan 2014

(Left-right) Nada Hamza Babiker, director, Commission of Biotechnology and Genetic Engineering, speaks during opening session; Joyce Nzioki, bioinformatics analyst, the BecA-ILRI Hub, gives support to workshop participants; Etienne De Villiers, scientist, Kenya Medical Research Institute (KEMRI) Wellcome Trust, Kilifi-Kenya prepares to facilitate a session

(Left-right) Ali Babiker, Assistant Professor, Plant Genetics Resources Unit-Agricultural Research Corporation pays attention during a lecture; H.E Alsadig Sabah Alkhair, State Minister of Science and Communications; Prof Migdam Elshekh Abdelgani, Director General, National Center for Research-Sudan; Joyce Nzioki, the BecA-ILRI Hub during the opening session; Mark Wamalwa, post-doctoral scientist in bioinformatics, the BecA-ILRI Hub, facilitates a session on bioinformatics

(Left-right) Ali Babiker, Assistant Professor, Plant Genetics Resources Unit-Agricultural Research Corporation pays attention during a lecture; H.E Alsadig Sabah Alkhair, State Minister of Science and Communications; Prof Migdam Elshekh Abdelgani, Director General, National Center for Research-Sudan; Joyce Nzioki, the BecA-ILRI Hub during the opening session; Mark Wamalwa, post-doctoral scientist in bioinformatics, the BecA-ILRI Hub, facilitates a session on bioinformatics

The workshop which attracted participants from 13 institutions in Sudan received support the Sudan Government and the National Centre for Research (NCR). Participants were introduced to the basic concepts of bioinformatics and the use of various tools for the analysis of complex genomic data; Next Generation Sequencing (NGS) technologies and the tools for NGS data analysis, data integration and visualization; multiple sequence analysis and phylogenetics; and sequence analysis using the eBiokit.

Participants to the workshop received the eBioKit, a complete kit of bioinformatics tools, enabling them to work independently from any location. The system runs multiple open source web services on an Apple Mac-mini where all databases are stored locally. The e-biokit reduces the need for fast internet connection while giving the users an opportunity to incorporate their data sets in widely used web services.

Sudan is among the eastern and central African countries where the BecA-ILRI Hub is expanding the base of expertise in agricultural research. Since 2011, over 10 national scientists from Sudan have had access to training in the latest agricultural bioscience technologies as they conducted research on the country’s priority areas addressing food and nutritional insecurity and livestock health.